Helios: A Scalable 3D Plant and Environmental Biophysical Modeling Framework.

Brian N Bailey

doi:10.3389/fpls.2019.01185

Abstract

This article presents an overview of Helios, a new three-dimensional (3D) plant and environmental modeling framework. Helios is a model coupling framework designed to provide maximum flexibility in integrating and running arbitrary 3D environmental system models. Users interact with Helios through a well-documented open-source C++ API. Version 1.0 comes with model plug-ins for radiation transport, the surface energy balance, stomatal conductance, photosynthesis, solar position, and procedural tree generation. Additional plug-ins are also available for visualizing model geometry and data and for processing and integrating LiDAR scanning data. Many of the plug-ins perform calculations on the graphics processing unit, which allows for efficient simulation of very large domains with high detail. An example modeling study is presented in which leaf-level heterogeneity in water usage and photosynthesis of an orchard is examined to understand how this leaf-scale variability contributes to whole-tree and -canopy fluxes.

Highlights

Biophysical processes in plant and environmental systems traverse an extraordinary range of spatial and temporal scales, with high heterogeneity commonly present across these scales
Homogeneity is assumed in all Helios Biophysical Modelling Framework directions including the vertical, which is convenient because it means that a measurement or model prediction at any point in space can be considered representative of the entire plant system
The primitive binning calculations are performed on the graphics processing unit (GPU) to significantly reduce execution times

Summary

Introduction

Biophysical processes in plant and environmental systems traverse an extraordinary range of spatial and temporal scales, with high heterogeneity commonly present across these scales. It is convenient to study plant systems at scales most relevant to humans—leaves to canopies in space and seconds to months in time Obtaining observations beyond these scales often requires high effort that may yield little additional useful information. On the other hand, when measurements are performed at large scales that aggregate many smaller scales, it is often unclear how different members of the community (i.e., leaves) contribute to aggregate behavior In this brief case study, a tree canopy will be examined using Helios to visualize and quantify leaf-level variability in transpiration and photosynthesis in order to understand how individual elements contribute to system-level behavior. The simulated trees had leaves with constant (one-sided) area of 60 cm

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Results

Conclusion